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- PDB-1rym: Structure of the Group II Intron Splicing Factor CRS2 -

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Basic information

Entry
Database: PDB / ID: 1rym
TitleStructure of the Group II Intron Splicing Factor CRS2
Componentsprotein CRS2
KeywordsTRANSLATION / ALPHA-BETA
Function / homology
Function and homology information


peptidyl-tRNA hydrolase activity / chloroplast stroma / RNA splicing / mRNA processing / tRNA binding / ribonucleoprotein complex
Similarity search - Function
: / Peptidyl-tRNA hydrolase / Peptidyl-tRNA hydrolase signature 1. / Peptidyl-tRNA hydrolase / Peptidyl-tRNA hydrolase, conserved site / Peptidyl-tRNA hydrolase superfamily / Peptidyl-tRNA hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chloroplastic group IIB intron splicing facilitator CRS2, chloroplastic
Similarity search - Component
Biological speciesZea mays (maize)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsOstheimer, G.J. / Barkan, A. / Matthews, B.W.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: Structural analysis of the group II intron splicing factor CRS2 yields insights into its protein and RNA interaction surfaces
Authors: Ostheimer, G.J. / Hadjivasiliou, H. / Kloer, D.P. / Barkan, A. / Matthews, B.W.
History
DepositionDec 22, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 6, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: protein CRS2


Theoretical massNumber of molelcules
Total (without water)23,6561
Polymers23,6561
Non-polymers00
Water2,234124
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.100, 79.600, 112.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Cell settingorthorhombic
Space group name H-MI222

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Components

#1: Protein protein CRS2


Mass: 23655.943 Da / Num. of mol.: 1 / Fragment: CRS2(E) / Mutation: I42E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zea mays (maize) / Gene: CRS2 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 Gold / References: UniProt: Q9M5P4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.76 Å3/Da / Density % sol: 55.1 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 10% PEG 3400, sodium citrate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
210 %PEG34001reservoir
3100 mMsodium citrate1reservoirpH5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 6, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. all: 22503 / Num. obs: 22475 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 6.9 % / Biso Wilson estimate: 21.1 Å2 / Rsym value: 0.069 / Net I/σ(I): 5.7
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 6.6 % / Mean I/σ(I) obs: 2.5 / Num. unique all: 21544 / Rsym value: 0.257 / % possible all: 99.9
Reflection
*PLUS
Lowest resolution: 15 Å / Rmerge(I) obs: 0.069
Reflection shell
*PLUS
% possible obs: 99.9 % / Rmerge(I) obs: 0.257

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
EPMRphasing
TNTrefinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: CRS2 residues through K178 (PTH numbering)

Resolution: 1.8→20 Å / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.259 1150 5 %RANDOM
Rwork0.19 ---
all0.195 22503 --
obs0.195 22475 99.9 %-
Solvent computationSolvent model: bulk solvent modelled with TNT / Bsol: 118 Å2 / ksol: 0.72 e/Å3
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1411 0 0 124 1535
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.014
X-RAY DIFFRACTIONt_angle_deg2.73
Refinement
*PLUS
Lowest resolution: 15 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.025
X-RAY DIFFRACTIONt_angle_deg2.8

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